ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CACCGCGACCTCAAGCCGGAGAACTTCCTCTTCGCCAATAAGAAGGAGAACTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcacaccaaccgagatcctttcccaaattcggacgattttctgcgcatcttcaaccgtgatttctggttttagtgggaggaaacttacttgacgg...

Basic information

species	Zea mays
transcript	GRMZM2G311220_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G311220_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g61590.1 (Oryza sativa), 5'ss of exon 1

CACCGCGACCTCAAGCCGGAGAACTTCCTCTTCGCCAATAAGAAGGAGAACTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcacacc-aaccgagatcctttcccaaattcggacgattttctgcgcatcttcaaccgtgatttctggttttagtgggaggaaacttacttgacgg-
||||| ||||||||||| |||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||| ||| || |   |  || |||||||| ||||||| |||| || ||| ||  | |    |   | |   || |          | |||    ||  | | | || 
CACCGGGACCTCAAGCCCGAGAACTTCCTCTTCGCCAACAAGAAGGAGAACTCGCCGCTCAAGGCCATCGATTTCGGCCTCTCCATCTTCTTCAAGCCCGgtaagccctgcagaatcgagatccgttcccaatttcgaacaattatccactcgcactt--ctgaatttccgtacagcctcgtgagatctctagcctaatggt

upper sequence: GRMZM2G311220_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA07G18310.1 (Glycine max), 5'ss of exon 1

CACCGCGACCTCAAGCCGGAGAACTTCCTCTTCGCCAATAAGAAGGAGAACTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcacaccaaccgagatcc--tttcccaaattcggacgattttctgcgcatcttcaac-cgtgattt--ctggttttagtgggaggaaacttacttgacgg
||||||||||||||||||||||||||| | ||||| || ||||||||||| |||||||||||||| || || || || |||||||| ||||||||||| |||  |       ||    ||| |  |||     |||  |  ||||   |  | |  ||  |   |||| ||  ||| | || || |  |||    |||| |  | 
CACCGCGACCTCAAGCCGGAGAACTTCTTGTTCGCGAACAAGAAGGAGAATTCGCCGCTCAAGGCAATTGATTTTGGCCTCTCCATATTCTTCAAGCCAGgtacgctg----aatttggattcggtttagtgcattgcgtggattcggtttggagtttggaggtgtgacttgtctgctgtttgtagttggatttctact-gttgt

upper sequence: GRMZM2G311220_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA18G43160.1 (Glycine max), 5'ss of exon 3

CACCGCGACCTCAAGCCGGAGAACTTCCTCTTCGCCAATAAGAAGGAGAACTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcacaccaaccgagatcc--tttcccaaattcggacgattttctgcgcatcttcaac-cgtgatttctgg--ttttagtgggaggaaacttacttgacgg
||||| ||||||||||||||||||||| | ||||| || ||||||||||| |||||||||||||| || ||||| || |||||||| ||||||||||| |||  |       ||    ||| |  |||     |||  |  |||||  |  | |  ||  |   |||  || ||   | ||  | |  |||    |||||||   
CACCGAGACCTCAAGCCGGAGAACTTCTTGTTCGCGAACAAGAAGGAGAATTCGCCGCTCAAGGCTATTGACTTTGGCCTCTCCATATTCTTCAAGCCAGgtacggtg----aatttggattcggtttagtgcattgtgtggatttggtttggagtttggaggtgtggcttgtgtgctgtttatagatggatttctacttgatt-

upper sequence: GRMZM2G311220_T03 (Zea mays), 5'ss of exon 1
lower sequence: EDP04678 (Chlamydomonas reinhardtii), 5'ss of exon 7

----CACCGCGACCTCAAGCCGGAGAACTTCCTCTTCGCCAATAAGAAGGAGAACTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTC-AAGCCTGgtgagtcacaccaaccgagatcctttcccaaattcggacgattttctgcgcatcttcaaccgtgatttctggttttagtgggaggaaacttacttgacgg
    ||||||||||| |||||||||||||||||  |  |  |       |      || |||| ||||| |  ||||||||||| ||   ||||||| | |   |  | |   | ||   ||  |||   |  | |||  ||  |    | ||     |  |  | | |||   || ||  |   |  |    |  |  ||    
CATTCACCGCGACCTGAAGCCGGAGAACTTCCTGCTGTCGGACCGCTCCGCCGCGGCGGCGCTGAAGGCGACGGACTTCGGTCTGTCGTCCTTCTTCCAGgtgcgcgggggtgctcctggcgc-atcgggtgaccaatggggcagtgggtttggaagacagcggcag-gatgcgtgtttgcaaccgtggcgtgcaaatgtgg---

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

ATGC    EST sequence
ATGC    genomic sequence (exon)
ATGC    genomic sequence (truncated intron)

EST: gi|149085145|gb|EE174649.2|EE174649

EST:     CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTG                         GTGAAAAAGTTTTCAGAAATTGGTGGGAAGCCCCTATTACATGGCTCCTGA
genomic: CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcaca ... tctactttagGTGAAAA-GTTTTCAGAAATTG-TGGGAAGCCCCTATTACATGGCTCCTGA

EST: gi|149102142|gb|EE287576.2|EE287576

EST:     CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTG                         GTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAG
genomic: CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcaca ... tctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAG

EST: gi|21432179|gb|BQ547669.1|BQ547669

EST:     CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTG                         GTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAG
genomic: CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcaca ... tctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAG

EST: gi|78119680|gb|DV538064.1|DV538064

EST:     CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTG                         GTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAG
genomic: CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcaca ... tctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAG

EST: gi|149113217|gb|EE288137.2|EE288137

EST:     CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTG                         GTGAAAAAGTTT-CAGAAATTGTGGGGAAGCCCCTATTACAT
genomic: CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcaca ... tctactttagGTGAAAA-GTTTTCAGAAATTGTGGG-AAGCCCCTATTACAT

EST: gi|71774878|gb|DR972756.1|DR972756

EST:     CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTG                         GTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCT
genomic: CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcaca ... tctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCT

EST: gi|78118424|gb|DV536810.1|DV536810

EST:     CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCTATCTTCTTCAAGCCTG                         GTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAG
genomic: CTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcaca ... tctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAG

RNA-Seq data

ATGC Supported by RNA-Seq exonic block that spans over the splice site

atgs Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.

Found data for 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

CACCGCGACCTCAAGCCGGAGAACTTCCTCTTCGCCAATAAGAAGGAGAACTCGCCGCTCAAGGCCATCGACTTCGGTCTCTCCATCTTCTTCAAGCCTGgtgagtcaca ... tctactttagGTGAAAAGTTTTCAGAAATTGTGGGAAGCCCCTATTACATGGCTCCTGAAGTATTGAAGAGAAACTATGGGCCAGAAATAGACATATGGAGTGCGGGAGT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 102